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Large-scale multivariate dataset on the characterization of microbiota diversity, microbial growth dynamics, metabolic spoilage volatilome and sensorial profiles of two industrially produced meat products subjected to
changes in lactate concentration and packaging atmosphere
Simon Poirier, Ngoc-Du Martin Luong, Valérie Anthoine, Sandrine Guillou, Jeanne-Marie Membré, Nicolas Moriceau, Sandrine Reze, Monique Zagorec,
Carole Feurer, Bastien Fremaux, et al.
To cite this version:
Simon Poirier, Ngoc-Du Martin Luong, Valérie Anthoine, Sandrine Guillou, Jeanne-Marie Membré,
et al.. Large-scale multivariate dataset on the characterization of microbiota diversity, microbial
growth dynamics, metabolic spoilage volatilome and sensorial profiles of two industrially produced
meat products subjected to changes in lactate concentration and packaging atmosphere. Data in
Brief, Elsevier, 2020, 30, pp.1-8. �10.1016/j.dib.2020.105453�. �hal-02914971�
ContentslistsavailableatScienceDirect
Data in Brief
journalhomepage:www.elsevier.com/locate/dib
Data Article
Large-scale multivariate dataset on the characterization of microbiota diversity, microbial growth dynamics, metabolic
spoilage volatilome and sensorial profiles of two industrially produced meat products subjected to changes in lactate concentration and packaging atmosphere
Simon Poirier
a,1, Ngoc-Du Martin Luong
b,1, Valérie Anthoine
b, Sandrine Guillou
b, Jeanne-Marie Membré
b, Nicolas Moriceau
b, Sandrine Rezé
b, Monique Zagorec
b, Carole Feurer
c,
Bastien Frémaux
c, Sabine Jeuge
c, Emeline Robieu
c, Marie Champomier-Vergès
a, Gwendoline Coeuret
a,
Emilie Cauchie
d, Georges Daube
d, Nicolas Korsak
d, Louis Coroller
e, Noémie Desriac
e, Marie-Hélène Desmonts
f, Rodérick Gohier
f, Dalal Werner
f, Valentin Loux
g,j, Olivier Rué
g,j,
Marie-Hélène Dohollou
h, Tatiana Defosse
i, Stéphane Chaillou
a,∗aINRAE, AgroParisTech, Micalis Institute, Université Paris-Saclay, 78350, Jouy-en-Josas, France
bINRAE, UMR1014 Secalim, Oniris, Nantes, France
cIFIP-Institut du Porc, Maisons-Alfort et Le Rheu, France
dVeterinary Medicine Faculty, Food Sciences, Université de Liège, FARAH, 40 0 0 Liège, Belgium
eUniversité de Bretagne Occidentale, EA3882 Lubem, Quimper, France
fAerial, 67412 Illkirch, France
gINRAE, MaIAGE, Université Paris-Saclay, 78350 Jouy-en-Josas, France
hCooperl, 22403 Lamballe, Armor, France
iCellule Recherche et Innovation, Groupe LDC, Sablé sur Sarthe, France
jINRAE, BioinfOmics, MIGALE bioinformatics facility, Université Paris-Saclay, 78350 Jouy-en-Josas, France
∗ Corresponding author.
E-mail address: stephane.chaillou@inrae.fr (S. Chaillou).
1These authors contributed equally as first authors to this work.
https://doi.org/10.1016/j.dib.2020.105453
2352-3409/© 2020 The Author(s). Published by Elsevier Inc. This is an open access article under the CC BY license.
( http://creativecommons.org/licenses/by/4.0/ )
2 S. Poirier, N.-D.M. Luong and V. Anthoine et al. / Data in Brief 30 (2020) 105453
a r t i c l e i n f o
Article history:
Received 10 February 2020 Revised 9 March 2020 Accepted 12 March 2020 Available online 20 March 2020 Keywords:
Meat spoilage Food microbiota Microbial ecology Metabolomic Metagenetic
a b s t r a c t
Data inthisarticle providedetailedinformation onthedi- versity of bacterial communities present on 576 samples of raw pork or poultry sausages produced industrially in 2017. Bacterial growth dynamics and diversity were mon- itored throughout the refrigerated storage period to esti- mate the impact of packaging atmosphere and the use of potassiumlactateaschemicalpreservative.Thedatainclude severaltypesofanalysis aimingatprovidingacomprehen- sive microbial ecology of spoilageduring storageand how the processparameters doinfluence thisphenomenon.The analysis includes: the gas content in packaging, pH, chro- mametricmeasurements,platecounts(totalmesophilicaer- obic flora and lactic acid bacteria), sensorial properties of theproducts,meta-metabolomicquantificationofvolatileor- ganiccompoundsandbacterialcommunitymetageneticanal- ysis. Bacterial diversity was monitored using two types of ampliconsequencing(16SrRNAandGyrBencodinggenes)at different timepointsforthedifferentconditions (576sam- ples for gyrBand 436 samples for 16S rDNA). Sequencing dataweregeneratedbyusingIlluminaMiSeq.Thesequenc- ingdatahavebeendepositedinthebioprojectPRJNA522361.
Samples accession numbers vary from SAMN10964863 to SAMN10965438forgyrBampliconandfromSAMN10970131 toSAMN10970566for16S.
© 2020TheAuthor(s).PublishedbyElsevierInc.
ThisisanopenaccessarticleundertheCCBYlicense.
(http://creativecommons.org/licenses/by/4.0/)
Specificationstable
Subject area Applied Microbiology and Biotechnology
More specific subject area Microbial ecology of food spoilage during industrial production.
Type of data Table, figure, raw sequencing data
How data was acquired Total aerobic mesophilic population was estimated on Plate Count Agar (PCA) (Oxoid, France) for pork, (Biomerieux, France) for poultry and on de Man, Rogosa, and Sharpe (MRS) agar (Oxoid, France) for pork, (Biomerieux, France) for poultry. Both media were incubated aerobically for 48 h at 30 °C to estimate the bacterial population size in CFU. g −1of meat. Gas composition of the trays was assessed for all trays with CheckMate3 (Dansensor, France) or Oxybaby O 2/CO 2analyzer (WITT, Germany) for pork and poultry sausages, respectively. The pH of sausages was measured using FiveGo FG2 with the electrode LE427-S7 (Mettler toledo, USA). Color (L ∗, a ∗, b ∗) was assessed using the Minolta CR400 ChromaMeter (Grosseron, France) in CIE-Lab scale. Volatile organic compounds (VOC) were determined by HS–GC–MS on a Varian 450 gas chromatograph (Varian, USA) coupled to a Varian 225-IT mass spectrometer (Varian), equipped with a CTC Combi PAL (CTC Analytics AG, Switzerland). Quantitative descriptive analysis (QDA) was performed using seven olfactory attributes by a trained sensory panel of 15 experts. DNA amplicon sequencing was carried out with Illumina MiSeq.
( continued on next page )
Data format Raw, analyzed
Parameters for data collection The type of meat used for production of sausage was the first parameter analyzed (raw pork sausages and raw poultry sausages). The second parameter was the time of storage from the raw meat material up to sausages at the end of storage (primary cuts, gut casing, spices and fat).
The third parameter was meat batch variability along ten sampling campaigns which were conducted for each meat product. Finally, we analyzed two process parameters: one was the influence of three doses of potassium lactate (complete dose, half dose or zero dose) used as preservative as well as three packaging atmospheres (air, and two modified atmospheres i.e. 70%O 2/30%CO 2and 50%N 2/50%CO 2,).
Description of data collection Meat samples were collected directly in two independent factories in France, just out of the production line. The large-scale sampling strategy was organized over a period of six months from July to December 2017.
Data source location Samples related to pork sausages were collected in Lamballe (France, latitude: 48.4667, longitude: −2.5167) while samples related to poultry sausages were collected in Sablé-sur-Sarthe (France, latitude: 47.8376, longitude: −0.3329).
Data accessibility Data are available as supplementary tables (Excel spreadsheets) at the institutional INRAE data repository: https://doi.org/10.15454/UDQLGE . The sequencing data have been deposited in the bioproject PRJNA522361.
Valueofthedata
• Thedataprovidealinkbetweenmeatspoilage(bacterialcounts,pH,color,volatilemetabolic spoilagecompounds non-targetedquantificationfurther referredas“volatilome” andsenso- rialprofiles),thepackagingatmosphere,andtheuseoflactateandmicrobiotacomposition.
• Sequencing data can be used to understand the variation of bacterialcommunity dynam- ics,abundanceanddiversityinthesetwomeatproductsaccordingtothetypeofmeatand packagingatmosphere,andtheuseoflactate.
• Sequencing datacan be usedto identify biomarkers of spoilage.Accessibility to 16S rDNA andgyrB OTU (Operational Taxonomic Unit) dataand detailedassociated metadata allows researcherstoperformnewanalyseswiththeirownresearchpurposes.
• Tenindependentsamplingcampaignswere conductedfortwomeatproducts.Awidenum- ber of conditions were tested (three lactate concentrations and three packaging atmo- spheres).Thislarge-scale samplingstrategy inwhich over550sampleswere sequenced,at fourdifferent time points(fromday 0to day22 ofstorage) provides aunique dataset for powerfulstatisticalanalysisofprocessparametersinfluencingrawmeatsausagespoilage.
1. Datadescription
In the EU 20% of the initial meat production is lost, more than half occurring at animal production, slaughtering, processing and distribution steps [1,2]. This crucial economic and environmental issueinfoodindustry isin partattributedtospoilage duringstorage,whichis the consequence ofbacterial growthand subsequentmetabolic activities causingorganoleptic changes of the final product unacceptable forhuman consumption (defects in texture, color, odor,tasteoraspect)[3].
Forindustrialmeatproducers,predictingaccurateused-by-datesfortheirproductsbasedon spoilageoccurrenceremains abigchallenge.Thelackoflarge-scalemultivariatedatagenerated andassociatedwithspecificmeatproductionsisone ofthegapsthatneeds tobefilledbefore suchchallengecouldbeovercome.Theobjectiveofthisprojectwasthustoprovidesuchdataset based on a large collaborative project betweenacademic partners, technical centers,and two industrial producers. Wecollected overa sixmonths productionperiod, muchcomprehensive information on thedynamics ofbacterial communities andphysico-chemical variables associ-
4 S. Poirier, N.-D.M. Luong and V. Anthoine et al. / Data in Brief 30 (2020) 105453
T0 =Day 2
n=3 n=9 n=9 n=9
Sausages x3 Lactate doses
x3 Packagings
T1 = Day 7
•Primal cuts
•Spices
•Gut casing
•Fat
Ti = Day 0
T2 = Day 15
Sausages x3 Lactate doses
x3 Packagings
T3 = Day 22
Sausages x3 Lactate doses
x3 Packagings
34 samples x 10 sampling campaigns x 2 meat product (poultry and pork) Meat Baer
x3 Lactate doses
Embossing and packaging
Poultry factory
INDUSTRIAL PRODUCTION
Pork factory
STORAGE AT 4°C AND 8°C
•Primal cuts
•Spices
•Gut casing
•Fat Meat baer x3 Lactate doses
n=4 (one of each)
pH, Packaging gas composion, Chromametry Enumeraon (Total aerobic mesophilic, Lacc acid bacteria)
Microbial DNA extracon
SHIPMENT AND FREEZING OF SAMPLES SHIPMENT AND
FREEZING OF DNA Microbiota analysis (amplicon sequencing 16S rDNA gyrB)
Meta-Omic data integraon
Sensory analysis Non-targeted metabolic
Volalome analysis
SHIPMENT 4°CSEIROTAROBALLACINHCET&CIMEDACAOT
Fig. 1. Large-scale strategy for the analysis of meat sausage samples and production of the dataset.
atedwithmeatspoilagealongtheprocessingsteps.Processedporkandpoultrymeat(sausages) were chosen as two examples of spoilage sensitive meat products that are among the most consumed in France. Products included all sausages ingredients (meat cuts, gut casing, spice mixes,andfat)tocoverthewholemeatprocess.Theexperimentalworkconsistedindetermin- ingthediversityandthedynamicsofbacterialcommunitiesduringfoodprocessingandstorage, andcorrelatingthem withspoilage occurrence.Inthe frameof thisproject,sensoryandnon- targetedmetabolicvolatilomeanalyseswereperformedinordertocharacterizethemeatprod- uctspoilageinrelationwithfoodprocessingfactorslikeconcentrationofchemicalpreservatives (potassiumlactate)andgascompositionofstoragepackaging.Theoriginalityofthisprojectwas to integrate biotic (microbialecology), abiotic (sensory attributes andstorage conditions) and temporal factors (monitoring along processing steps) to generate heterogeneous multivariate dataforused-by-date predictivemathematical models.Fig. 1illustrates theglobalexperimen- tal designof thisstudy. Links tosupplementary data(available asspreadsheets) presented in Table1includeall themetadatacharacterizingeach sample,aswell asthe samplesthatwere selectedforthedifferentanalyses(16SrDNAsequencing,gyrBsequencing,volatilomeandsen- sorialprofile).
2. Experimentaldesign,materialsandmethods 2.1. Experimentaldesignandsampling
The project focused on the monitoring of two food matrices: pork sausages and poultry sausages.Forpork sausages, two typesofmeat pieces were used: normalmid shoulder meat anddefatted/boneless/derindedshoulder meat(also named shoulder4D). Forpoultrysausage, the meat was from turkey. In both sausages, pork fat was added to a final content of 20%
and 11% in pork and poultry sausages, respectively. The following additives were added in
Table 1
List of supplementary tables (Tables available as spreadsheets at https://doi.org/10.15454/UDQLGE ) making up the dataset.
Table S1 Sample nomenclature and metadata associated with each sample.
Table S2 pH dynamics over time for the different meat products.
Table S3 Chromametric measures for the different meat products.
Table S4 Gas composition (%) of the packaging atmosphere over time for the different meat products Table S5 Total mesophilic aerobic flora (log 10CFU. g −1) over time for the different meat products Table S6 Lactic acid bacteria (log 10CFU. g −1) over time for the different meat products
Table S7 Non-targeted metabolic volatilome composition (reduced centered normalization of pic areas) over time for the different meat products
Table S8 Sensorial profiles over time for the different meat products
Table S9 Microbial diversity analysis based on 16S rDNA V3-V4 region amplicon sequencing including OTU abundance table, OTU taxonomic assignment table and samples metadata table usable for phyloseq R package analysis [4] .
Table S10 Microbial diversity analysis based on gyrB amplicon sequencing including OTU abundance table, OTU taxonomic assignment table and samples metadata table usable for phyloseq R package analysis [4] .
pork sausages: potassium lactate(1.13% w/w, corresponding to full normal dose); sodium ac- etate 0.27%(w/w); sodiumascorbate0.06% (w/w). In poultrysausagesthe followingadditives wereadded:potassiumlactate(2.0%w/w,correspondingtofullnormaldose).Furthermore,both sausages werebattered withaspicemix asingredientaddedto aconcentration of∼2.5% and containing(sodiumsalt∼40%,dextrose ∼10%, spices ∼15%, aromas∼22%).Tensamplingcam- paignswereconductedduring6monthsontheproductionchainsoftwosausageproducersin order to get a sufficient number ofindependent biological replicates. For each campaign and each foodmatrix, identicalsamplingstrategy was applied.Four typesof samplescorrespond- ing to the ingredients constituting sausages were collected: primal cuts, gut casing, fat and spices.
Three meat batters were separately prepared with different doses of lactate (the nor- mal dose routinely used by the industrials, half of this dose and without any lactate). The three meat batters were sampled before their embossing into the tubular gut casing. Pork sausages were packedimmediately after embossing whereas poultry sausages were packed 2 days later. Sausages were separately packagedby five into trays under three different atmo- spheres(normalair;50%CO2-50%N2;and70%O2-30%N2),sealedwiththinhighbarrierpolyester- basedfilm PET/EVOH (Co-polymerof EthyleneandVinyl alcohol)/PE(PolyEthylene) andstored during the first 5 days at 4°C and then until the end of the incubation at 8°C. The phys- ical properties of the packaging were as follows: oxygen transmission rate <5 cm3/m2·24 h−1·bar−1, CO2 transmission rate <25 cm3/m2. During storage, sausages were sampled at three differentdates: day 7,day15, andday 22(which wasconsidered as an abusedstorage time).
Trayswerefrozenat−20°Cpriorcolor,sensory,andVOCanalyses.Othertreatmentsoranal- yseswereperformeddirectly.
2.2. Physico-chemicalanalyses
Forall samplespH measureswere performedonthree sausagesper trayusingFiveGo FG2 withthe electrodeLE427-S7 (Mettler toledo,USA) insertedin sausages.Forpork sausagesgas composition of each tray was assessed with CheckMate3 (Dansensor, France). The same pro- cedure wasapplied for poultrysausages with a digital O2/CO2 Oxybaby analyzer (WITT,Ger- many).Visualcolorchangeswereevaluatedintriplicatesforeachcondition,eachsamplingtime andeach production batchusing theMinolta CR400ChromaMeter (Grosseron,France) in CIE- Labscale.ThemeasurementsdeterminedchromaticcoordinatesofL∗(brightness),a∗(green-red balance)andb∗(blue-yellowbalance).
6 S. Poirier, N.-D.M. Luong and V. Anthoine et al. / Data in Brief 30 (2020) 105453 2.3.Bacterialcollection
Ten to fifty grams of each food-product batch were mixedin a 400ml stomacher bag of 280μm (Interscience BagPage, France) with 4 vol (40 to 200mL) of BK018HA peptone water (Biokar Diagnostics, France) supplemented with 1% V/V Tween 80 (VWR Chemicals, France).
Mixes were treated for 3min (pork) or 2min (poultry) in a Masticator Homogenizator (IUL, Spain).Then, 32mL of theshreds were collectedandcentrifuged at 500×g for 3minat 4°C tospindownthefoodmatrixfibersanddebris.Thestill-turbidsupernatant(∼25mL)wascol- lectedandcentrifugedat3000×g(pork)or10,000xg(poultry)for5minat4°Ctospindown thebacterial cells. The bacterialpellet thus obtainedwaswashed in 1mL ofsterile ultrapure water andcollected after centrifugation as above for 5min at 4°C to serve directly for DNA extractionorforplating.
3. Plating
Bacterialcounts were estimated fromfiltrates obtained after thestomaching step andfol- lowing the ISO 4833-1:2013 and ISO 15214:1998 methods. Serial dilutions in peptone water were performedand plated on Plate CountAgar (PCA)(Oxoid, France) for pork, (Biomerieux, France) for poultryand on de Man, Rogosa, and Sharpe (MRS)agar (Oxoid,France) forpork, (Biomerieux,France)forpoultryandincubatedaerobicallyfor48hat30°Ctoestimatethetotal aerobicmesophilicpopulationandthemesophiliclacticacidbacteriapopulationsizeinCFUg−1 ofmeat,respectively.
3.1. DNAextraction,amplificationandsequencing
Total DNA was extracted from bacterial pellets obtained after stomaching and a cen- trifugation steps using DNeasy PowerFood Microbial Kit (Mobio Laboratories, USA) accord- ing to the manufacturer’s instructions and as described in Poirier et al. [5]. DNA extracts were used forthe amplification of the bacterialhypervariable region V3–V4of the 16S rRNA gene withthe primers V3F(5-ACGGRAGGCWGCAGT-3) andV4R (5-TACCAGGGTATCTAATCCT- 3). In parallel,the degeneratedprimers F64 (5-MGNCCNGSNATGTAYATHGG-3) andR353 (5- CNCCRTGNARDCCDCCNGA-3)wereusedtoamplifya∼280-bpregionofgyrBgeneasdescribed inPoirieret al.[5]. Sequencingwasperformed byGenoscreen (France) onIllumina Miseq se- quencerusingtheMiSeqReagentKitv3(2×250bppaired-endreads).
3.2.Sequencereadprocessing,OTUclusteringandtaxonomicassignments
Paired-endsequencesweremergedandtrimmedasdescribedpreviously[5].Dataweresub- sequentlyimportedintotheFROGS(FindRapidlyOTUswithGalaxySolution)pipeline[6]tobe cleaned,filtered, clusteredintoOperationalTaxonomicunitsandtaxonomically assignedusing theSilva128SSUdatabase[7]andahomemadegyrBdatabase[5].
3.3.Sensorydescriptiveanalysis
Samplesofpoultryandporksausages,previouslystoredat−20°C,wereone-nightdefrostin acoldroom. Justbeforeanalysis, about50g ofsampleweretransferred intoa250mLopaque glassvial and sealedwith a glass stopper. Asensory panel of expertsin profiling techniques (n=15;atleast5previousexperiencesonfoodsensoryanalysiswithprofilingtechniques)were
trainedduring8months(minimum15h)onalteredporkandpoultrysausages.Duringtraining, they developedaconsensus vocabularyinordertoseparateimportantattributesdescribingal- teredsausagesoff-odorcomparedtonon-alteredones.Sameattributeswerechosenforporkand poultrysausages.Quantitative descriptive analysis(QDA)[8]wasperformedusingthose seven olfactoryattributes.Thedifferentattributesandtheirrespectivedescriptorsusedfortheevalua- tionofthesampleswereglobalalterationodor,rancid,eggy/sulfurous,ethereal/fermentedfruit, fermented/old drysausage,old cheese,sour/pungent. TheQDAwasperformedintensessions.
Eachpanelistreceivedrandomly12codedsamplesinasession.Sampleswerepresentedmonad- icallyaccordingtoabalanceddesigninvialscontainingsausageforsniffing.Sensory evaluation wascarriedoutatroomtemperature(25±2°C)inisolatedboothsinasensorylab.Eachpanelist ratedtheglobalalterationodorintensityandthe6odorattributesintensitiesofeachsampleon a10cmunstructuredlinescale(from“absent” to“very intense”)withsensoryevaluationsoft- ware(FizzBiosystems,France).
3.4. Volatileorganiccompound(VOC)analysis
Samplesofpoultryandporksausages,previouslystoredat−20°C,werecutinsmallpiecesin acoldroomtominimizethevolatilizationofVOC.Around3–4gofsampleweretransferredinto a 20mL headspacevialandsealedwithascrewcap withsilicone rubberseptum.The vialwas weightedbefore and aftersamplingto determine the exactweight of sausage.Analyses were carriedoutintriplicate.VOCweredeterminedbyHS–GC–MS.Allanalyseswereperformedona Varian450gaschromatograph(Varian,USA)coupledtoaVarian225-ITmassspectrometer(Var- ian),equippedwithaCTCCombiPAL(CTCAnalyticsAG,Switzerland).Sampleswereequilibrated byagitationat60°Cfor20minpriortoinjectionand1mLwasdrawledfromtheheadspaceto injectintheGC.TheHS-GC–MSconditionswereasfollows:capillarycolumn:DB-624UI(30m x 0.25mm I.D×1.4mm film thickness) (Agilent Technologies, USA); Carrier gas: Helium with a flow rateof 1.4mL.min−1; Injection port mode: splitless; Needle temperature: 60°C; Injec- tion temperature:220°C.The oven temperaturewasprogrammed froman initialtemperature of40°C(7minholding), risingto50°Cat4°C/min (1minholding), to70°Cat4°C/min(1min holding),to120°Cat3°C/min(2minholding)andto245°Cat30°C/min(4minholding).Trans- ferlinetemperature:250°C.Thetemperaturesofthemanifoldandtheiontrapwerekeptcon- stantat150°Cand40°Crespectively. Datawere obtainedinscan mode atfour scans/sinthe mass range(m/z) of35–350 atomicmass units.VOCwere identified by comparisonofGCre- tentiontimesandmassspectrawiththoseofthestandard compounds.Peakarea (inUA) was usedasquantitativedatatomonitortherelativechangesofVOCoverstorage,potassiumlactate concentration andatmospherepackaging. Datawere initiallysubjectedtopre-processingusing thestandardnormalvariatetransformationtofacilitatecomparisonofthepeakswithdifferent magnitudes.
ConflictofInterest
The authorsdeclarethat they havenoknown competingfinancialinterests orpersonal re- lationships which have, or could be perceived to have, influenced the work reported in this article. This work was supported by the ANR RedLosses Project, Grant ANR-16-CE21-0006, operated by the French Agence Nationale de la Recherche. SP and NDML were granted for postdoctoral and PhDstudy respectively through this agency. The funding body didnot play any role neither in the design of the study nor in collection, analysis, and interpretation of data.
8 S. Poirier, N.-D.M. Luong and V. Anthoine et al. / Data in Brief 30 (2020) 105453 Acknowledgments
The authors express their gratitude to the INRAE MIGALE bioinformatics facility (MIGALE, INRAE,2020.MigalebioinformaticsFacility,doi:10.15454/1.5572390655343293E12)forproviding computationalresourcesanddatastorage.
Supplementarymaterials
Supplementarymaterial associated withthisarticlecan be found,inthe onlineversion, at doi:10.1016/j.dib.2020.105453.
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